| URL: | http://www.3dmet.dna.affrc.go.jp |
| Full name: | Three-dimensional structure database of natural metabolites |
| Description: | This database has not only 3D-structures but also some descriptors. Each structures are searchable by these descriptors. This system also has a simple search system for substructure of the molecule. The search can be perfomed by three levels depending on the accuracy. |
| Year founded: | 2013 |
| Last update: | |
| Version: | |
| Accessibility: |
Accessible
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| Country/Region: | Japan |
| Data type: | |
| Data object: |
NA
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| Database category: | |
| Major species: |
NA
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| Keywords: |
| University/Institution: | National Institute of Agrobiological Sciences |
| Address: | |
| City: | |
| Province/State: | |
| Country/Region: | Japan |
| Contact name (PI/Team): | Miki H. Maeda |
| Contact email (PI/Helpdesk): | mmaeda@nias.affrc.go.jp |
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Three-dimensional structure database of natural metabolites (3DMET): a novel database of curated 3D structures. [PMID: 23293959]
A database of 3D structures of natural metabolites has been developed called 3DMET. During the process of structure conversion from 2D to 3D, we found many structures were misconverted at chiral atoms and bonds. Several popular converters were tested in regard to their conversion accuracy. For verification, three canonical strings were also tested. No procedure could satisfactorily cover all the structures of the natural products. The misconverted structures had to be corrected manually. However, a nonnegligible number of mistakes were also observed even after manual curation, so a self-checking system was developed and introduced to our work flow. Thus, the 3D structures in our 3DMET database were evaluated in two steps: automatically and manually. The current version includes most of the natural products of the KEGG COMPOUND collection [ http://www.genome.jp/kegg/compound/ ] and is searchable by string, value range, and substructure. 3DMET can be accessed via http://www.3dmet.dna.affrc.go.jp/ , which also has detailed manuals. |